Neutrino-Nucleus Reactions and Muon Capture in 12C

The neutrino-nucleus cross section and the muon capture rate are discussed within a simple formalism which facilitates the nuclear structure calculations. The corresponding formulae only depend on four types of nuclear matrix elements, which are currently used in the nuclear beta decay. We have also considered the non-locality effects arising from the velocity-dependent terms in the hadronic current. We show that for both observables in 12C the higher order relativistic corrections are of the order of ~5 only, and therefore do not play a significant role. As nuclear model framework we use the projected QRPA (PQRPA) and show that the number projection plays a crucial role in removing the degeneracy between the proton-neutron two quasiparticle states at the level of the mean field. Comparison is done with both the experimental data and the previous shell model calculations. Possible consequences of the present study on the determination of the $\nu_\mu ->\nu_e$ neutrino oscillation probability are briefly addressed.Comment: 29 pages, 6 figures, Revtex4. Several changes were made to the previous manuscript, the results and final conclusions remain unalterable. It has been accepted for publication as a Regular Article in Physical Review

Environmental shaping of codon usage and functional adaptation across microbial communities.

Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community

Measurement of Inverse Pion Photoproduction at Energies Spanning the N(1440) Resonance

Differential cross sections for the process pi^- p -> gamma n have been measured at Brookhaven National Laboratory's Alternating Gradient Synchrotron with the Crystal Ball multiphoton spectrometer. Measurements were made at 18 pion momenta from 238 to 748 MeV/c, corresponding to E_gamma for the inverse reaction from 285 to 769 MeV. The data have been used to evaluate the gamma n multipoles in the vicinity of the N(1440) resonance. We compare our data and multipoles to previous determinations. A new three-parameter SAID fit yields 36 +/- 7 (GeV)^-1/2 X 10^-3 for the A^n_1/2 amplitude of the P_11.Comment: 14 pages, 8 figures, submitted to PR

Ratios of Elastic Scattering of Pions from 3H and 3He

We have measured the elastic-scattering ratios of normalized yields for charged pions from 3H and 3He in the backward hemisphere. At 180 MeV, we completed the angular distribution begun with our earlier measurements, adding six data points in the angular range of 119 deg to 169 deg in the pi-nucleus center of mass. We also measured an excitation function with data points at 142, 180, 220, and 256 MeV incident pion energy at the largest achievable angle for each energy between 160 deg and 170 deg in the pi-nucleus center of mass. This excitation function corresponds to the energies of our forward-hemisphere studies. The data, taken as a whole, show an apparent role reversal of the two charge-symmetric ratios r1 and r2 in the backward hemisphere. Also, for data > 100 deg we observe a strong dependence on the four-momentum transfer squared (-t) for all of the ratios regardless of pion energy or scattering angle, and we find that the superratio R data match very well with calculations based on the forward-hemisphere data that predicts the value of the difference between the even-nucleon radii of 3H and 3He. Comparisons are also made with recent calculations incorporating different wave functions and double scattering models.Comment: RevTex 8pages, 12 figure file

Neutron skin of 208^{208}Pb from Coherent Pion Photoproduction

Information on the size and shape of the neutron skin on $^{208}$Pb has been extracted from coherent pion photoproduction cross sections measured using the Crystal Ball together with the Glasgow tagger at the MAMI electron beam facility. On exploitation of an interpolated fit of a theoretical model to the measured cross sections the half-height radius and diffuseness of the neutron distribution are found to be 6.70$\pm 0.03(stat)$ fm and 0.55$\pm 0.01(stat)$$^{+0.02}_{-0.03}(sys)$ fm respectively, corresponding to a neutron skin thickness $\Delta r_{np}$=0.15$\pm 0.03(stat)$$^{+0.01}_{-0.03}(sys)$ fm. The results give the first successful extraction of a neutron skin with an electromagnetic probe and indicate the skin of $^{208}$Pb has a halo character. The measurement provides valuable new constraints on both the structure of nuclei and the equation of state for neutron-rich matter.Comment: 4 figures 5 pages. Version submitted to journal. Includes additional studies of systematic effects in the extracted diffuseness, which led to a small increase in the quoted systematic error. These additional studies are discussed in the revised manuscript. Also includes minor editorial improvements to the tex

Determination of the Dalitz plot parameter alpha for the decay eta->3pi^0 with the Crystal Ball at MAMI-B

A precise measurement of the Dalitz plot parameter, alpha, for the eta->3pi^0 decay is presented. The experiment was performed with the Crystal Ball and TAPS large acceptance photon detectors at the tagged photon beam facility of the MAMI-B electron accelerator in Mainz. High statistics of 1.8*10^6 eta->3pi^0 events were obtained, giving the result alpha = -0.032 +/- 0.002(stat) +/- 0.002(syst).Comment: 9 pages, 6 figures, published in the online-first section of EPJ A, included changes referees asked for, added DO

Precise Measurement of the Pi+ -> Pi0 e+ nu Branching Ratio

Using a large acceptance calorimeter and a stopped pion beam we have made a precise measurement of the rare Pi+ -> Pi0 e+ Nu,(pi_beta) decay branching ratio. We have evaluated the branching ratio by normalizing the number of observed pi_beta decays to the number of observed Pi+ -> e+ Nu, (pi_{e2}) decays. We find the value of Gamma(Pi+ -> Pi0 e+ Nu)/Gamma(total) = [1.036 +/- 0.004(stat.) +/- 0.004(syst.) +/- 0.003(pi_{e2})] x 10^{-8}$, where the first uncertainty is statistical, the second systematic, and the third is the pi_{e2} branching ratio uncertainty. Our result agrees well with the Standard Model prediction.Comment: 4 pages, 5 figures, 1 table, revtex4; changed content; updated analysi

Design, Commissioning and Performance of the PIBETA Detector at PSI

We describe the design, construction and performance of the PIBETA detector built for the precise measurement of the branching ratio of pion beta decay, pi+ -> pi0 e+ nu, at the Paul Scherrer Institute. The central part of the detector is a 240-module spherical pure CsI calorimeter covering 3*pi sr solid angle. The calorimeter is supplemented with an active collimator/beam degrader system, an active segmented plastic target, a pair of low-mass cylindrical wire chambers and a 20-element cylindrical plastic scintillator hodoscope. The whole detector system is housed inside a temperature-controlled lead brick enclosure which in turn is lined with cosmic muon plastic veto counters. Commissioning and calibration data were taken during two three-month beam periods in 1999/2000 with pi+ stopping rates between 1.3*E3 pi+/s and 1.3*E6 pi+/s. We examine the timing, energy and angular detector resolution for photons, positrons and protons in the energy range of 5-150 MeV, as well as the response of the detector to cosmic muons. We illustrate the detector signatures for the assorted rare pion and muon decays and their associated backgrounds.Comment: 117 pages, 48 Postscript figures, 5 tables, Elsevier LaTeX, submitted to Nucl. Instrum. Meth.

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

BACKGROUND: Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species. RESULTS: This paper describes EasyBack, a new parameter-free, fully-automated software for backtranslation using Hidden Markov Models. EasyBack is not based on imitation of codon usage within the target species, but instead uses a sequence-similarity criterion. The model is trained with a set of proteins with known cDNA coding sequences, constructed from the input protein by querying the NCBI databases with BLAST. Unlike existing software, the proposed method allows the quality of prediction to be estimated. When tested on a group of proteins that show different degrees of sequence conservation, EasyBack outperforms other published methods in terms of precision. CONCLUSION: The prediction quality of a protein backtranslation methis markedly increased by replacing the criterion of most used codon in the same species with a Hidden Markov Model trained with a set of most similar sequences from all species. Moreover, the proposed method allows the quality of prediction to be estimated probabilistically